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Articles by Hideyuki Doi
High-frequency eDNA metabarcoding survey data of coastal fish across the Japanese Archipelago
Abstract The Japanese archipelago, spanning over 3,000 km from subarctic to subtropical zones (approximately 24°N to 45°N), hosts a diverse array of coastal fish communities shaped by pronounced latitudinal gradients. Here, we present a high-frequency environmental DNA (eDNA) metabarcoding dataset of coastal fishes collected across the archipelago.
Urban Stressors Disrupt the Phenological Clock, Unravelling Urban Ecosystems and Services
Abstract Urban environments impose unique stressors, urban heat islands, artificial light at night, nitrogen deposition, and noise pollution, that disrupt the phenological rhythms of flora and fauna. Urban planning must shift from static greening to dynamic management of environmental cues.
Macroecological assessment of invasive species impact on Japanese lake fish communities using eDNA metabarcoding
Abstract Biological invasion has negative effects on ecological interaction such as competition and predation. The ecological impacts on native communities may also affect two processes that are important in determining community structures, namely, the environmental and spatial processes.
Does Allometric Scaling Improve Estimates of Population Abundance Based on Environmental DNA?
1 Introduction Detection of macro-organisms (e.g., fish, vertebrates and macroinvertebrates) from environmental DNA (eDNA) has become a popular tool for non-invasive and cost-effective monitoring of species distribution and diversity in a range of ecosystem types (terrestrial, freshwater and marine systems) (Minamoto 2022; Altermatt et al. 2025).
Large-scale environmental DNA survey reveals niche axes of a regional coastal fish community - Scientific Reports
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Abstract The concept of the ecological niche, defined as the basic habitat requirements for a species, is central to understanding species geographic distributions and predicting their responses to environmental change. However, identifying the essential niche for large regional communities remains a challenge because niche axes can be “hidden” by the complexity of the underlying ecological processes.
By Yutaka Osada, Masaki Miya, Hitoshi Araki, Hideyuki Doi, Akihide Kasai, Reiji Masuda, Toshifumi Minamoto, Teruhiko Takahara, Satoshi Yamamoto, Hiroki Yamanaka, Keiichi Fukaya, Takehiko Fukuchi, Ryo Gotoh, Masakazu Hori, Midori Iida, Tadashi Kajita, Takashi Kanbe, Tanaka Kenta, Yumi Kobayashi, Hiroki Mizumoto, Hiroyuki Motomura, Hiroaki Murakami, Kenji Nohara, Shin-ichiro Oka, Tetsuya Sado, Hiroshi Senou, Tomoki Sunobe, Hiroshi Takahashi Verified, Koji Takayama, Satoru Yokoyama, Seokjin Yoon, Michio Kondoh, Satoquo Seino, Mitsuhiro Aizu-Hirano, Tomohito Imaizumi, Tomohiko Matsuura, Koichi Shibukawa, Katsuhiko Tanaka, Hisashi Yamakawa
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Nature
Verified
Nitrogen deposition reveals global patterns in plant and animal stoichiometry - Nature Communications
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Abstract The elemental content of organisms links cellular biochemistry to ecological processes, from physiology to nutrient dynamics. While plant stoichiometry is thought to vary with climate and nutrient availability across latitudes, the consistency of these patterns across trophic groups and realms remains unclear.
By Angelica Gonzalez, Angélica González, Julian Merder, Karl Andraczek, Ulrich Brose, W. Stanley Harpole, Helmut Hillebrand, Michelle Jackson, Malte Jochum, Shawn Leroux, Mark Nessel, Renske E. Onstein, Rachel E. Paseka, Judith Sitters, Eugenia Zandonà, Attila Mozsár, Sarah L. Bluhm, Hideyuki Doi, Nico Eisenhauer, Vinicius F Farjalla, James Hood Verified, Pavel Kratina, Catherine E. Lovelock, Jean-Marc Roussel, Stefan Scheu, Julia Seeber, Michael Steinwandter, Alexei V. Tiunov, Melanie E. Pollierer
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Nature
Verified
Revealing Long-Term Multi-Factor Climate Impacts on Antarctic Phytoplankton: A Trend-Based Approach Using STL and Piecewise SEM
Abstract Climate change imposes multiple interacting stressors on ocean ecosystems. The Southern Ocean is among the regions where these impacts are particularly pronounced. Phytoplankton, which perform the bulk of primary production, both maintain the Antarctic marine food web and contribute to the role of the Southern Ocean as the largest oceanic sink for atmospheric CO2.
StoichLife: A Global Dataset of Plant and Animal Elemental Content - Scientific Data
Abstract The elemental content of life is a key trait shaping ecology and evolution, yet organismal stoichiometry has largely been studied on a case-by-case basis. This limitation has hindered our ability to identify broad patterns and mechanisms across taxa and ecosystems. To address this, we present StoichLife, a global dataset of 28,049 records from 5,876 species spanning terrestrial, freshwater, and marine realms.
Tributary mitigates river discontinuity by dam depending on the distance from dam to the tributary confluence
CONFLICT OF INTEREST STATEMENT The authors declare no conflicts of interest Supporting Information Filename Description rra4221-sup-0001-Supinfo.pdfPDF document, 134.4 KB Fig. S1. Biplot and Pearson's correlation coefficients (p>0.05) of the explanatory factors in Fig. 5, including tributary distance, watershed area (WSA) ratio, discharge ratio, % sand, and % gravel. The curved line indicates the data distribution of the factors. REFERENCES , & (2007).
Ethical considerations for human sequences in environmental DNA - Nature Ecology & Evolution
The analysis of environmental DNA (eDNA) is a rapidly developing field with great potential and as-yet-undreamed-of uses in conservation and ecology1,2,3. Residual genetic information from environmental samples can reveal species distributions and genotypes4,5,6, among other information about the living elements of ecosystems.
Predator‐induced plasticity in relation to prey body size: A meta‐analysis of Daphnia experiments
Evidence of publication bias We qualitatively analysed the funnel plot asymmetry of effect sizes and standard errors and found that several effect sizes fell outside the 95% CIs (Chaoborus: HL, TL, DM, Egg #) (Figure ). The number of studies or quantity of data for these traits may not be sufficient. In general, studies tend to publish only significantly different results of control and predator treatment.
Species traits and ecosystem characteristics affect species detection by eDNA metabarcoding in lake fish communities
ORIGINAL ARTICLE Hideyuki Doi, Shunsuke Matsuoka and Shin-ichiro S. Matsuzaki contributed equally to this study. Abstract Although environmental DNA (eDNA) metabarcoding is an exceptionally useful and powerful tool for monitoring biodiversity, little is known about whether the traits of organisms and their ecosystem characteristics affect eDNA metabarcoding performance. Nationwide surveys can provide more detailed insights, yet such studies have rarely been conducted.
Sedimentary DNA can reveal the past population dynamics of a pelagic copepod
Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website.
A Biodiversity Boost From the Eurasian Beaver (Castor fiber) in Germany’s Oldest National Park
Impact Factor 4.171 | CiteScore 3.6 More on impact › TABLE OF CONTENTS 1Bavarian Forest National Park, Grafenau, Germany 2Forest Nature Conservation, Northwest German Forest Research Institute, Hann.
Author Correction: Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique
Author Correction: Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique Author Correction Open Access Published: 01 June 2021 Scientific Reports volume 11, Article number: 11953 (2021) Cite this article The Original Article was published on 23 February 2021 Correction to: Scientific Reports https://doi.org/10.1038/s41598-021-83318-6, published online 23 February 2021 In this Article, the authors neglected to include a...
A unified framework for herbivore-to-producer biomass ratio reveals the relative influence of four ecological factors
Abstract The biomass ratio of herbivores to primary producers reflects the structure of a community. Four primary factors have been proposed to affect this ratio, including production rate, defense traits and nutrient contents of producers, and predation by carnivores. However, identifying the joint effects of these factors across natural communities has been elusive, in part because of the lack of a framework for examining their effects simultaneously.
Global diversity of microbial communities in marine sediment
Global diversity of microbial communities in marine sediment Tatsuhiko Hoshino, Hideyuki Doi, Go-Ichiro Uramoto, Lars Wörmer, Rishi R. Adhikari, Nan Xiao, Yuki Morono, Steven D’Hondt, Kai-Uwe Hinrichs, Fumio Inagaki Proceedings of the National Academy of Sciences Oct 2020, 201919139; DOI: 10.1073/pnas.1919139117
Formation of global self-beliefs in the human brain | Proceedings of the National Academy of Sciences
Significance Momentary feelings of confidence accompany many of our actions and decisions. In addition to such “local” feelings of confidence, we also construct “global” confidence estimates about our skills and abilities (global self-performance estimates or SPEs). Distorted SPEs may have a pervasive impact on motivation and self-evaluation, for instance affecting estimates of our competitiveness at work or in a sports team.
Exploring a legendary giant squid: an environmental DNA approach
Abstract The giant squid, Architeuthis dux, has been reported for centuries, but its distribution and ecology have remained famously mysterious. We investigated the A. dux distribution in the Sea of Japan using the environmental DNA (eDNA) method, which has recently been considered as a useful technique for evaluating the distributions of rare species. To develop the eDNA method to detect A.
Sedimentary DNA tracks decadal-centennial changes in fish abundance
Abstract Far too little is known about the long-term dynamics of populations for almost all macro-organisms. Here, we examined the utility of sedimentary DNA techniques to reconstruct the dynamics in the “abundance” of a species, which has not been previously defined. We used fish DNA in marine sediments and examined whether it could be used to track the past dynamics of pelagic fish abundance in marine waters.
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